Anvilicious: Being an "eco-goth" band, the song "Earth, Wind, Fire, and Air" is thick on its message on the importance of being environmentally friendly. It's still very catchy nevertheless.
Awesome Music: While Zombie Island delved into the punk genre, Witch's Ghost delved into gothic-themed Grunge with the Hex Girls. They provide some of the best music of the movie. Not as great as Zombie Island's music, but it's still great nonetheless.
Scooby and Shaggy successfully tailing the mayor and evading detection. At one point they do a Fakeout Makeout when he gets suspicious.
The Reveal that Ben was Evil All Along doubles as this and as Nightmare Fuel. He then takes the book, makes the huge announcement, calls out the Mayor and Thorn's dad for using Sarah's image horribly, and starts doing magic. Scary? Yes. Awesome? Hell yes.
When the Scooby Gang realizes that Ben was evil and used them to get Sarah's book of witchcraft, they immediately use their brains to steal the book from him for as long as they can. This results in their best display of teamwork and Character Development compared to Zombie Island, where they nearly got killed.
Also though it fails, Shaggy plucking up his courage to douse Sarah with water, hoping it would melt her like in The Wizard of Oz. Especially considering this is Shaggy.
Also the entire gang playing Keep Away with the book as Sarah's magic incapacitates them long enough for Thorn to get the book and read it.
Ensemble Darkhorse: The Hex Girls proved to be very popular and have become recurring characters in the franchise ever since.
As noted under Artistic License – Religion, Thorn being 1/16th Wiccan is complete nonsense. However she still clearly practices some elements of Wicca which arguably still makes her the best chance to defeat Sarah.
Also, Ben Ravencroft first heard about Mystery Inc from their solving the mystery of the "Moat Monster". The Moat Monster was the same story that Daphne brought up in her interview towards the beginning of Zombie Island, which means 'The Witch's Ghost' takes place in the same universe as 'Zombie Island'.